/hwfssz4/BC_COM_P5/F17FTSNCKF1543/SORcsaD/input//Lib_500bp_1.fq.gz /hwfssz4/BC_COM_P5/F17FTSNCKF1543/SORcsaD/input//Lib_500bp_2.fq.gz|/share/backup/xujiabao/Software/Samtools/samtools-1.3.1/samtools view -b -S - |/share/backup/xujiabao/Software/Samtools/samtools-1.3.1/samtools sort - -o /hwfssz4/BC_COM_P5/F17FTSNCKF1543/SORcsaD/S16.Pilon/S353_qual33_hq_after_DBG2OLC_time2/bwa//Lib_500.sort.bam 
/share/backup/xujiabao/Software/Samtools/samtools-1.3.1/samtools index /hwfssz4/BC_COM_P5/F17FTSNCKF1543/SORcsaD/S16.Pilon/S353_qual33_hq_after_DBG2OLC_time2/bwa//Lib_500.sort.bam
java -Xmx300G -jar /share/backup/xujiabao/Software/Pilon/pilon-1.22.jar --genome   S353_qual33_hq_after_DBG2OLC_time2/pilon/final_assembly.fasta  --frags S353_qual33_hq_after_DBG2OLC_time2/bwa/result/Lib_270.sort.bam  --frags  S353_qual33_hq_after_DBG2OLC_time2/bwa/result/Lib_500.sort.bam   --output S353_Pilon_after_DBG2OLC --threads 40